Team Leader
Shigehiro Kuraku
Ph.D.
Laboratory for Phyloinformatics
[Closed Mar. 2023]
E-mailshigehiro.kuraku[at]riken.jp
Please replace [at] with @.
The ‘genome’ stands for a complete set of genetic information per species (or cell) that is a blueprint of our body structure and biological processes at different levels. The genome was not suddenly created but is an interim product of successive modifications over billion years. Every single genome has a history embedded in DNA sequences, and comparisons of the information between species provide clues for past evolutionary events.
By making use of cutting-edge DNA sequencing technologies and bioinformatics, we conduct molecular-level analysis on diversity and evolution of genomes and epigenomes of vertebrates. Our activity includes taking an initiative in whole genome sequencing and analysis projects for some important vertebrate species, which is leading to our fostering of biodiversity literacy from viewpoints of genomics and molecular evolution.
Research Theme
- Biodiversity research based on understanding of life sciences and molecular evolutionary approaches
- Improvement of genome analysis techniques for chromosome-scale DNA sequencing
- Vertebrate evolutionary genomics encompassing chromatin organization and regulation
- Decoding genomes of important organisms with little molecular information
Selected Publications
Ohnishi T, Kiyama Y, Arima-Yoshida F, et al.
Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia.
EMBO molecular medicine
13(4), e12574 Fri Apr 09 00:00:00 JST 2021
doi: 10.15252/emmm.202012574
Kajikawa E, Horo U, Ide T, et al.
Nodal paralogues underlie distinct mechanisms for visceral left-right asymmetry in reptiles and mammals.
Nature ecology & evolution
4(2), 261-269 Sat Feb 01 00:00:00 JST 2020
doi: 10.1038/s41559-019-1072-2
Kadota M, Nishimura O, Miura H, et al.
Multifaceted Hi-C benchmarking: what makes a difference in chromosome-scale genome scaffolding?
GigaScience
9(1), giz158 Wed Jan 01 00:00:00 JST 2020
doi: 10.1093/gigascience/giz158
Kishida T, Go Y, Tatsumoto S, et al.
Loss of olfaction in sea snakes provides new perspectives on the aquatic adaptation of amniotes.
Proceedings. Biological sciences
286(1910), 20191828 Wed Sep 11 00:00:00 JST 2019
doi: 10.1098/rspb.2019.1828
Hara Y, Takeuchi M, Kageyama Y, et al.
Madagascar ground gecko genome analysis characterizes asymmetric fates of duplicated genes.
BMC Biology
16, 40 Sat Dec 01 00:00:00 JST 2018
doi: 10.1186/s12915-018-0509-4
Hara Y, Yamaguchi K, Onimaru K, et al.
Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates.
Nature ecology & evolution
2(11), 1761-1771 Thu Nov 01 00:00:00 JST 2018
doi: 10.1038/s41559-018-0673-5
Onimaru K, Kuraku S.
Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.
Briefings in functional genomics
17(5), 352-361 Thu Sep 27 00:00:00 JST 2018
doi: 10.1093/bfgp/ely008
Nishimura O, Hara Y, Kuraku S.
gVolante for standardizing completeness assessment of genome and transcriptome assemblies.
Bioinformatics
33(22), 3635-3637 Fri Dec 01 00:00:00 JST 2017
doi: 10.1093/bioinformatics/btx445
Kadota M, Hara Y, Tanaka K, et al.
CTCF binding landscape in jawless fish with reference to Hox cluster evolution.
Scientific Reports
7(1), 4957 Wed Nov 01 00:00:00 JST 2017
doi: 10.1038/s41598-017-04506-x
Smith JJ, Kuraku S, Holt C, et al.
Sequencing of the sea lamprey (Petromyzon marinus) genome provide insights into vertebrate evolution.
Nature Genetics
45(4), 415-421 Sun Dec 01 00:00:00 JST 2013
doi: 10.1038/ng.2568
Kuraku S.
Impact of asymmetric gene repertoire between cyclostomes and gnathostomes.
Seminars in Cell and Developmental Biology
24(2), 119-127 Fri Nov 01 00:00:00 JST 2013
doi: 10.1016/j.semcdb.2012.12.009
Kuraku S, Zmasek CM, Nishimura O, Katoh K.
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
Nucleic acids research
41(Web Server issue), W22-8 Mon Jul 01 00:00:00 JST 2013
doi: 10.1093/nar/gkt389
Members
Mitsutaka Kadota
Technical Scientist
Osamu Nishimura
Technical Scientist
Chiharu Tanegashima
Expert Technician
Kaori Tatsumi
Technical Staff II
Yuta Ohishi
Junior Research Associate
